• AP2-domain
• bZIP (Basic Leucine Zipper)
• bZIP_MAF (Basic Leucine Zipper/Maf Extended Homology Region transcription factor)
• CBFB NFYA (CCAAT-binding transcription factor subunit B)
• CTF NFI (CCAAT-box-binding factor/Nuclear Factor I)
• CUT
• E2F_TDP (E2F/DP family winged-helix DNA-binding domain)
• Ets (Erythroblast Transformation Specific Domain)
• Fork_head
• GATA (GATA zinc finger)
• HALZ (Homeobox associated leucine zipper)
• HLH (Helix-loop-helix DNA-binding domain)
• HMG_box (High Mobility Group box)
• HNF-1 N (Hepatocyte nuclear factor 1, amino terminus)
• Homeobox
• HSF DNA-bind (Heat Shock Factor-type DNA-binding)
• IRF (Interferon regulatory factor transcription factor)
• MH1 (MAD homology 1 domain)
• Myb DNA-binding (Myb-like DNA-binding domain)
• Myc N term (Myc amino-terminal region)
• PAX (Paried box domain)
• PBX (PBC)
• POU
• RFX DNA binding (Regulatory Factor binding to X box DNA binding domain)
• RHD (Rel Homology Domain)
• Runt
• SRF-TF (Serum Response Factor-type transcription factor)
• STAT bind (Signal Transducers and Activators of Transcription protein DNA-binding domain)
• TBP (Transcription factor RFIID/TATA-binding protein)
• TEA (Transcriptional Enhancer Activators/ATTS domain family)
• TF AP-2 (Transcription Factor Activator Protein 2)
• TF Otx (Otx1 Transcription Factor)
• WRKY
• zf-C4 (Zinc Finger, C4 type/Nuclear Hormone Receptor)
• zf-Dof (Dof domain, zinc finger)
• Zn Clus (Fungal Zn(2)-Cys(6) binuclear cluster domain)

PFAM acc#	PFAM family	#	Logo	Ambiguity Code	Found with
PF00847	AP2-domain	# 1		GGgAw.yGTGy	AlignAce
PF00170	bZIP Basic Leucine Zipper	# 2		s.TGACGy	AlignAce
PF00170	bZIP	# 3		Tkr.GyMA	AlignAce
PF00170	bZIP	# 4		TGAsTCAs	AlignAce
PF00170	bZIP	# 5		caCGTGgc	AlignAce
PF00170	bZIP	# 6		TGCAAyms	AlignAce
PF00170	bZIP	# 7		mCACGTGk	DimerFinder
PF00170	bZIP	# 8		aTGACGTCAt	DimerFinder
PF00170	bZIP	# 9		aTGAsTCAt	DimerFinder
PF00170	bZIP	#10		aTTg..cAAt	DimerFinder
PF00170	bZIP	#11		gcCACGTGgc	DimerFinder
PF00170	bZIP	#12		gTGacGTG	DimerFinder
PF00170	bZIP	#13		TkACGTmA	DimerFinder
PF03131	bZIP_Maf Basic Leucine Zipper/Maf Extended Homology Region Transcription Factor	#14		GCtgaGTCA	AlignAce (top ranked 28.8)
PF03131	bZIP_Maf	#15		TGAsTCA	DimerFinder
PF02045	CBFB_NFYA CCAAT-binding transcription factor subunit B	#16		CCAAysrg	AlignAce (top ranked 32.9)
PF00859	CTF_NFI CCAAT-box-binding factor/Nuclear Factor I	#17		tTGSC...	AlignAce
PF00859	CTF_NFI	#18		TGGc.....gCCA	DimerFinder
PF02376	CUT	#19		..ATyGRT	AlignAce
PF02376	CUT	#20		CgATcG	DimerFinder
PF02376	CUT	#21		cgATCGAT	DimerFinder
PF02319	E2F_TDP E2F/DP(Dimerization Partners) family winged helix DNA-binding domain	#22		GCGssAAa	AlignAce
PF00178	Ets Erythroblast Transformation Specific Domain	#23		smGGAagy	AlignAce
PF00250	Fork_head	#24		rYAAACAa	AlignAce
PF00250	Fork_head	#25		AryMAATA	AlignAce
PF00250	Fork_head	#26		AATATT	DimerFinder
PF00250	Fork_head	#27		kTTGTT	DimerFinder
PF00250	Fork_head	#28		TGTTTrTT	DimerFinder
PF00250	Fork_head	#29		TTTrTTTA	DimerFinder
PF00320	GATA GATA zinc finger	#30		.mGAyArG	AlignAce
PF00320	GATA	#31		yGATArs.	AlignAce
PF02183	HALZ Homeobox associated leucine zipper	#32		AAT.ATTG	AlignAce
PF02183	HALZ	#33		cAAT.ATTg	DimerFinder
PF00010	HLH Helix-loop-helix DNA-binding domain	#34		s.CrsGTG	AlignAce
PF00010	HLH	#35		CAgcTG	DimerFinder
PF00010	HLH	#36		cCACGTGg	DimerFinder
PF00010	HLH	#37		tCACGTGa	DimerFinder
PF00505	HMG_box High Mobility Group box	#38		AACAAwRr	AlignAce
PF04814	HNF-1_N Hepatocyte nuclear factor 1, N terminus	#39		g.yRAw.ATTAAC	AlignAce
PF04814	HNF-1_N	#40		GtTAAT.ATTAaC	DimerFinder
PF00046	homeobox	#41		TAAKKrss	AlignAce
PF00046	homeobox	#42		AAgyrcTT	DimerFinder
PF00046	homeobox	#43		AaT.AtT	DimerFinder
PF00046	homeobox	#44		TAATt.aATTA	DimerFinder
PF00046	homeobox	#45		TAATTAat	DimerFinder
PF00447	HSF_DNA-bind Heat Shock Factor-type DNA binding	#46		GAA..YTCkmG	AlignAce
PF00447	HSF_DNA-bind	#47		GAA..TTC	DimerFinder
PF00447	HSF_DNA-bind	#48		TTCtaGAA	DimerFinder
PF00447	HSF_DNA-bind	#49		TTCyaGAAg.TTC	DimerFinder
PF00605	IRF Interferon regulatory factor transcription factor	#50		gAAA.yGAAAs	AlignAce
PF00605	IRF	#51		sTTTCrcTTT	DimerFinder
PF00605	IRF	#52		gTTTCrsTTTC	DimerFinder
PF03165	MH1 MAD homology 1 domain	#53		tGGCw...	AlignAce
PF03165	MH1	#54		TGGc.....gCCA	DimerFinder
PF00249	myb_DNA-binding Myb-like DNA-binding domain	#55		yAACsG.c	AlignAce
PF00249	myb_DNA-binding	#56		CATaCAT	DimerFinder
PF00249	myb_DNA-binding	#57		GGTwGGT	DimerFinder
PF01056	Myc_N_term Myc animo-terminal region	#58		CACGTGs..	AlignAce
PF01056	Myc_N_term	#59		cCACGTGg	DimerFinder
PF00292	PAX Paired box domain	#60		raSCgKGrm	AlignAce
PF00292	PAX	#61		CGT.ACG	DimerFinder
PF00292	PAX	#62		TCA.gc.TGA	DimerFinder
PF03792	PBX Now called PBC	#63		tGATTGAT	AlignAce
PF03792	PBX	#64		TGATTGAT	DimerFinder
PF00157	pou Pou domain- N-terminal to homeobox domain	#65		ATGCAAAT	AlignAce
PF00157	pou	#66		ATGmATaw	AlignAce
PF00157	pou	#67		ATAAwTTAT	DimerFinder
PF02257	RFX_DNA_binding RFX (Regulatory Factor binding to X box) DNA-binding domain	#68		GTTGCcr.G..rm	AlignAce (top ranked 38.0)
PF00554	RHD Rel Homology Domain	#69		GGrAa.yCCc	AlignAce
PF00554	RHD	#70		GGaawttCC	DimerFinder
PF00554	RHD	#71		GGawwtCC	DimerFinder
PF00554	RHD	#72		GGGGAwTCCCC	DimerFinder
PF00853	Runt	#73		yTGyGGT.	AlignAce
PF00319	SRF-TF Serum Response Factor-type transcription factor	#74		CCwwAwaTrG	AlignAce
PF00319	SRF-TF	#75		CTATwwATAG	DimerFinder
PF00319	SRF-TF	#76		tCCwTwwAwGGa	DimerFinder
PF02864	STAT_bind STAT(Signal Transducers and Activators of Transcription) protein DNA-binding domain	#77		TTCy.GGAA	AlignAce
PF02864	STAT_bind	#78		TTyC..GrAA	DimerFinder
PF02864	STAT_bind	#79		wTTCy.rGAAw	DimerFinder
PF00352	TBP Transcription factor TFIID/TATA-binding protein	#80		G.ATATAwA	AlignAce
PF00352	TBP	#81		TATwTAT	DimerFinder
PF01285	TEA Transcriptional Enhancer Activators/ATTS domain family	#82		GGAATG.rr	AlignAce
PF03299	TF_AP-2 Transcription Factor Activator Protein 2	#83		GsSwssgss	AlignAce (top ranked 30.9)
PF03529	TF_Otx Otx1 Transcription Factor	#84		kgrGaTTAgtg	AlignAce (top ranked 24.9)
PF03106	WRKY	#85		cgGtCamcg	AlignAce
PF00105	zf-C4 Zinc finger, C4 type/Nuclear Hormone Receptor	#86		..rGGTCA	AlignAce
PF00105	zf-C4	#87		aGaACA...TGTtCt	DimerFinder
PF00105	zf-C4	#88		AGGTCAc.gTGACCT	DimerFinder
PF00105	zf-C4	#89		AGGTCATGACCT	DimerFinder
PF00105	zf-C4	#90		tcAAGkTCAag	DimerFinder
PF00105	zf-C4	#91		TGACCT...kTGACCT	DimerFinder
PF00105	zf-C4	#92		TGACCTTTGACCyy	DimerFinder
PF02701	zf-Dof Dof domain, Zinc finger	#93		...wAAAG.	AlignAce
PF00172	Zn_clus Fungal Zn(2)-Cys(6) binuclear cluster domain	#94		CGG..g..	AlignAce (top ranked 29.3)
PF00172	Zn_clus	#95		CGGa..acwgt..tCCG	DimerFinder

Top ranked:This motif is the top ranked motif produced by AlignACE for this family, but does not meet our significance threshold (Enrichment = 40).

In a number of cases, a motif found by AlignACE is similar to a motif found by DimerFinder. For example, motifs #4 and #9 in the bZIP family and #50 and #52 in the IRF family. We have not attempted to remove these redundancies.